Multiple windows is easy to ignore if you don't want it, but especially with the side-by-side multitasking view it's very nice to be able to group app instances together as they relate to things you're working on, and not sweating the fact that there can only be one web browser window.
For instance, if I'm doing research on something, I might have Notes or MindNode running with a copy of Safari paired alongside it. Those research related tabs are kept in their own world, not mixed with my main Safari instance and it's accumulated tabs.
And then let's say I'm writing an email about my travel plans and want to pull up the airline's website to look at my reservation. I can do that in a separate Safari instance instead of taking away the research sidebar from next to my MindNode document.
And the new Mail message can be its own window while I write it. If I need to refer to another message in my inbox, I don't have to close the draft I'm writing to get back to my inbox, and then go fetch it out of the drafts folder when I want to get back to it. Just swipe over to the main Mail window and swipe back when I'm done.
Or take an app like GoodNotes, where I have several notebooks on different subjects. I can open two of them at once instead of having to close notebook A, open notebook B, make a note, close notebook B, reopen notebook A every time I want to jot a quick note down in a different topic.
There's an adjustment period if you want to get in the habit of thinking about the iPad this way. But being able to operate it in terms of different tasks and projects, leaving their workspaces intact and unpolluted to come back to later, is a much more productive setup than having to play "How can I best allocate my single instance of the text editor?"